vector<string> setParameters();
string getCommandName() { return "dist.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
string getDescription() { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
bool abort, allLines, subsample;
set<string> labels; //holds labels to be used
- string outputFile, calc, groups, label, outputDir;
+ string outputFile, calc, groups, label, outputDir, mode;
vector<string> Estimators, Groups, outputNames; //holds estimators to be used
int process(vector<SharedRAbundVector*>, string, string);
int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);